This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. LANGSTON UNIVERSITY SCHOOL OF ARTS AND SCIENCES DEPARTMENT OF BIOLOGY INTRODUCTION TO BIOINFORMATICS BI4133 FALL SEMESTER, 2007 FACULTY Dr. Sharon Lewis - 307 Hamilton Hall - (405) 466-3316 salewis@lunet.edu OFFICE HOURS: MW from 10:00-3:00 p.m. OFFICE HOURS: Friday from 10:00-12:00 p.m. Dr. George Acquaah [unreadable]404 Research Building - (405) 466-6145 gacquaah@lunet.edu OFFICE HOURS: MWF from 10:00-11:00 a.m. Dr. Kanyand Matand [unreadable]235 Research Building - (405) 466-6131 kmatand@luresext.edu OFFICE HOURS: MWF 10-1:00 p.m. Mr. Theophilus Depona- 219 Hamilton Hall [unreadable](405) 466-3557 tadepona@lunet.edu OFFICE HOURS: MWF 2-5 p.m. OFFICE HOURS: T Th 8-10 a.m. Organization Lecture Laboratory Days Tuesday Thursday Time 1-2:15 1-2:15 Room Research Bldg, rm 405 HamH 316A REQUIRED TEXT and MATERIALS Journal articles will be assigned for this class. CATALOG DESCRIPTION Bioinformatics is a collection of methods used for analyzing molecular biology data with a computer. A team of Langston University faculty from various disciplines (chemistry, biology, mathematics, computer science, and research) will teach this course with the goal of cultivating research-oriented minority students for careers in bioinformatics. Interested students can compete for summer internships at PSC. RATIONALE Bioinformatics is an area of research developing as a result of the Human Genome Initiative and the advent of the World Wide Web, shortly thereafter. Once patented technology such as the polymerase chain reaction and the DNA sequencer were developed, molecular biologist began sequencing entire genomes from human, rat, and mouse to plants, such as rice and Arabidopsis, to microorganisms such as E. coli and Bacillus subtilis. The scientist quickly realized that someone needed to provide tools for collection, storage, and analysis of this exponentially growing amount of nucleotide sequences. Computer scientist were needed to write scripts to allow for the assembly of entire genomes and comparison of genes within the genomes and between genomes (rat with human with mosquitos. Computer scientist quickly realized that mathematicians were needed for the intricate details of statistics, algorithms, and matrices. Bioinformatics is a multi-disciplinary field that is constantly evolving to meet the demands of the post-genomic area, if there is one, aiming for the diminishless field of personalized medicine. COURSE OBJECTIVES The student should: 1. Define Bioinformatics and understand how this discipline evolved. 2. Complete the Unix Operating System Hands- On Exercise. 3. Retrieve Sequences from Databases and Complete Hands- On Exercise. 4. Complete the Database Searching and Alignment Hands-On Exercise. 5. Complete the Multiple Sequence Alignment Hands-On Exercise. 6. Complete the Pattern Identification and Matching Hands-On Exercise. 7. Complete the Python Exercises. 8. Complete the Phylogenetic Analysis Hands-On Exercises. 9. Complete the Finding Features in Groups of Sequences Hands-On Exercises. METHOD OF INSTRUCTION This class will be taught by a team of faculty who have experience in their fields of research. The faculty will use hands-on exercises, powerpoint presentations, and journal articles when presenting their information. COURSE REQUIREMENTS Each student should: 1. Attend all classes, punctually. 2. Complete all hands-on exercises. Take all exams or quizzes. 3. Complete your project. 4. Present your project. METHOD OF EVALUATION- Points for course requirements Each faculty member will assess the students as the subject matter lends itself. Minimum Grade Requirement: A = 90%;B = 80%;C = 70%;D = 60%;F = below 59% 3. Class Attendance It is imperative that students attend all lectures and labs. Material covered during each session is critical and is prerequisite to subsequent material. Material missed in one lecture can seriously hinder the student(s ability to comprehend related material. An attendance sheet will circulate at the beginning of class. Classes will be held daily. If no laboratory assignments are scheduled, then classes will be held in the recitation room. Six (6) absentees can result in an administrative withdrawal. The Office of Academic Affairs will give excused absences in the following two areas ONLY: Participation in University Functions (Who is on the Football Team?), and illness as documented with an official statement from the attending physician. Academic Integrity- NO CHEATING The following will apply to cases of academic dishonesty. The instructor ordinarily has final authority over the grades given to students or the lowering of grades because of cheating or plagiarism. If it is established by clear and convincing evidence that cheating or plagiarism has occurred, a) The instructor will take appropriate academic disciplinary action which may include the awarding of an "F" on the particular assignment or in the course. b) The instructor will make a report of the incident and of action taken, if any, to the departmental chair, the Vice President for Academic Affairs, Vice President for Student Affairs, and the student. c) The Student Disciplinary Committee may review the incident and impose conduct discipline, including conduct probation and suspension. d) The student may, if he/she so desires, discuss the matter with the Student Disciplinary Committee and/or the Student Judicial Court. Policy on Electronic Devices in the Classroom-NO CELLPHONES RINGING DURING TEST All electronic devices (e.g., cell phones, pagers, palm pilots, beeper watches) are considered unnecessary distractions and are to be turned off and (with the exception of watches) concealed during class. Thus, interacting with these devices during class will not be tolerated. Instructors may make exceptions for instructional purposes. A student who anticipates an emergency and expects to be contacted in class by an outside source must go directly through the emergency dispatch system identified on each of the respective campuses. The emergency dispatcher will take the message and deliver it to the instructor. A student who fails to comply with this policy will be initially dismissed from the class and (per the Instructor's discretion) may be counted absent. Points may be deducted for work missed during that time. A student who violates this policy a second time will be dropped from the course for disruptive behavior. A student whose electronic device is activated during an exam will be dismissed from the class and denied the opportunity to complete or take that exam. An Instructor may elect not to grade that exam. Langston University: Vision Statement Langston University, a land grant Historically Black institution of higher learning, will continue its rich tradition of developing leaders from a diverse, multi-cultural student body through excellent teaching, research, community service and public and private sector partnerships. As Langston University moves from Excellence to Greatness, it will be recognized for providing solutions to problems facing underserved populations in Oklahoma, the nation, and the world. Langston University: Core Values 1. Strong work ethic and dedication: We are united in our dedication to working as hard and as long as necessary in order to realize our vision of developing creative solutions to the problems facing undeserved populations in Oklahoma, the nation and the world. 2. Passion for learning: Our zeal for knowledge, our quest to understand "why" and our desire to develop innovative answers, create a vibrant academic community. 3. Courage to have exemplary character: We are building a community in which high ethical and moral standards are maintained and valued by our faculty, staff, and students. 4. Excellence: We value, treasure and reward excellence in scholarship, teaching, and community service. 5. Scholarly innovation and a commitment to scholarship: We are a community of pragmatic intellectuals, using our knowledge to better our state, nation and the world. 6. Appreciation of difference: We believe firmly that everyone must be respected and that there is always more that one way to consider any issue. We value diversity of opinions, ideas, cultures, and perspectives. 7. Fiscal accountability: We believe that solid fiscal management is the foundation upon which a great university is built. 8. Social responsibility: We believe that knowledge is a gift which must be used to create a better world. 9. Commitment to fundamental human rights: Above all, we value the right of every human being to enjoy freedom, respect, and the opportunity to realize his or her potential. AFFIRMATIVE ACTION Langston University, in compliance with Title VI and VII of the Civil Rights Acts of 1964, Executive Order 11246 as amended, Title IX of the Educational Amendments of 1972, Americans with Disabilities Act of 1990, and other federal laws and regulations, does not discriminate on the basis of race, color, national origin, sex, age, religion, handicap, or status as a veteran in any of its policies, practices, or procedures. This includes, but is not limited to, admissions, employment, financial aid, and educational services. ADA STATEMENT Langston University fully subscribes to all required standards of The Americans with Disabilities Act of 1990 (ADA). Persons in need of assistance should contact The ADA Compliance Officer in the Office of Student Affairs, Room 119, Page Hall, (405) 466-3445. This should be reported at some point before, during, or immediately after the first scheduled class period so accommodations can be provided for the student to be successful in that class. SCHEDULE: WEEK DATE MATERIAL COVERED 1 8/20 21-Aug Introduction to Bioinformatics and Introduction of Faculty-Dr. Lewis 22-Aug 23-Aug DOE movie and Installing Programs on Computers-Dr. Lewis 24-Aug 2 8/27 28-Aug DNA, Genes, Proteins Biology Overview-Dr. Acquaah 29-Aug 30-Aug DNA, Genes, Proteins Biology Overview-Dr. Acquaah 31-Aug 3 9/3 Labor Day Holiday 4-Sep Genomes-Dr. Lewis 5-Sep 6-Sep Genomes-Dr. Matand/ Hands-On Exercises-Mr. Depona 7-Sep 4 9/10 11-Sep New Sequence Analysis-Dr. Lewis, Dr. Bucki 12-Sep 13-Sep New Sequence Analysis-Dr. Matand/ Hands-On Exercises-Mr. Depona 14-Sep 5 9/17 18-Sep Pairwise Alignment and Sequence Database Searches: Algorithm-Dr. Hugh Nicholas 19-Sep 20-Sep Evaluation-Dr. Jimmy Torres/ Hands-On Exercises-Mr. Depona 21-Sep 6 9/24 25-Sep Database_Search_Significance-Dr. Lewis, Dr. Bucki 26-Sep 27-Sep Database_Search_Significance-Dr. Matand/ Hands-On Exercises-Mr. Depona 28-Sep 7 10/1 2-Oct Database_Search-Matrices-Dr. Matand 3-Oct 4-Oct Applied Database Searching-Dr. Lewis, Hands-On Exercises-Mr. Depona 5-Oct Homecoming Break 8 10/8 Homecoming Break 9-Oct Mutiple Sequence Alignment-Dr. Hugh Nicholas-PSC 10-Oct Midterm Exam Period 11-Oct Mutiple Sequence Alignment-Examples-Dr. Hugh Nicholas-PSC 12-Oct 9 10/15 16-Oct Multiple Sequence Alignment Hands-on-Alex Ropelewski 17-Oct 18-Oct Introduction to Mathematical Methods- Mr. Depona 19-Oct 10 10/22 23-Oct Introduction to Mathematical Models in Computational Biology and Bioinformatics-Mr. Depona, Hands-On Exercises-Mr. Depona 24-Oct 25-Oct Hands-On Exercises-Mr. Depona 26-Oct 11 10/29 30-Oct Aldehyde Dehydrogenase Motifs, Bioinformatics, Structure, Function and Genetics-Dr. Acquaah 31-Oct 1-Nov Hands-On Exercises-Mr. Depona 2-Nov 12 11/5 6-Nov Analysis of Isozymes-Dr. Acquaah 7-Nov 8-Nov Your Project 9-Nov 13 11/12 13-Nov Your Project 14-Nov 15-Nov Your Project 16-Nov 14 11/19 20-Nov Your Project 21-Nov Last Day to Drop a class and receive a